Starting phenix.real_space_refine on Fri Jun 27 18:20:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fql_29392/06_2025/8fql_29392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fql_29392/06_2025/8fql_29392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fql_29392/06_2025/8fql_29392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fql_29392/06_2025/8fql_29392.map" model { file = "/net/cci-nas-00/data/ceres_data/8fql_29392/06_2025/8fql_29392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fql_29392/06_2025/8fql_29392.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 20592 2.51 5 N 5736 2.21 5 O 6144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 286 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32652 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "C" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "D" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "E" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "F" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "G" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "H" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "I" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "K" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "L" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Time building chain proxies: 19.39, per 1000 atoms: 0.59 Number of scatterers: 32652 At special positions: 0 Unit cell: (152.28, 154.44, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 6144 8.00 N 5736 7.00 C 20592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.38 Conformation dependent library (CDL) restraints added in 4.5 seconds 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7704 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 48 sheets defined 50.9% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LYS A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 removed outlier: 4.267A pdb=" N GLU A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 296 removed outlier: 3.975A pdb=" N SER A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 326 Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 60 through 77 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 removed outlier: 4.482A pdb=" N VAL B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 296 removed outlier: 5.176A pdb=" N ARG B 284 " --> pdb=" O MET B 280 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP B 390 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 60 through 77 Processing helix chain 'C' and resid 97 through 105 Processing helix chain 'C' and resid 112 through 128 Processing helix chain 'C' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE C 199 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LYS C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 4.156A pdb=" N GLU C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 296 removed outlier: 3.613A pdb=" N VAL C 288 " --> pdb=" O ARG C 284 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 326 Processing helix chain 'C' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 364 through 377 Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP C 390 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 60 through 77 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 112 through 128 Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 247 removed outlier: 3.663A pdb=" N GLN D 242 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL D 243 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 296 removed outlier: 5.279A pdb=" N ARG D 284 " --> pdb=" O MET D 280 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D 290 " --> pdb=" O PHE D 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL D 302 " --> pdb=" O PRO D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 326 Processing helix chain 'D' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP D 390 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 112 through 128 Processing helix chain 'E' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE E 199 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LYS E 202 " --> pdb=" O ALA E 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE E 218 " --> pdb=" O GLN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 247 removed outlier: 3.663A pdb=" N GLU E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU E 245 " --> pdb=" O SER E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 252 removed outlier: 4.042A pdb=" N ALA E 251 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 296 removed outlier: 3.597A pdb=" N ARG E 284 " --> pdb=" O MET E 280 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU E 290 " --> pdb=" O PHE E 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 364 through 377 Processing helix chain 'E' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP E 390 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 60 through 77 Processing helix chain 'F' and resid 97 through 105 Processing helix chain 'F' and resid 112 through 128 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'F' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE F 199 " --> pdb=" O SER F 195 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LYS F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER F 203 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 218 " --> pdb=" O GLN F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 246 removed outlier: 4.197A pdb=" N VAL F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 296 removed outlier: 5.176A pdb=" N ARG F 284 " --> pdb=" O MET F 280 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL F 288 " --> pdb=" O ARG F 284 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 290 " --> pdb=" O PHE F 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 Processing helix chain 'F' and resid 327 through 342 removed outlier: 3.860A pdb=" N ILE F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP F 390 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 60 through 77 Processing helix chain 'G' and resid 97 through 105 Processing helix chain 'G' and resid 112 through 128 Processing helix chain 'G' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER G 203 " --> pdb=" O PHE G 199 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE G 218 " --> pdb=" O GLN G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 247 removed outlier: 3.823A pdb=" N GLU G 244 " --> pdb=" O ARG G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 252 removed outlier: 4.189A pdb=" N ALA G 251 " --> pdb=" O LYS G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 296 removed outlier: 3.684A pdb=" N ARG G 284 " --> pdb=" O MET G 280 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS G 285 " --> pdb=" O MET G 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL G 288 " --> pdb=" O ARG G 284 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU G 290 " --> pdb=" O PHE G 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE G 294 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE G 295 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 326 Processing helix chain 'G' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE G 331 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 357 through 362 Processing helix chain 'G' and resid 364 through 377 Processing helix chain 'G' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP G 390 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 60 through 77 Processing helix chain 'H' and resid 97 through 105 Processing helix chain 'H' and resid 112 through 128 Processing helix chain 'H' and resid 149 through 151 No H-bonds generated for 'chain 'H' and resid 149 through 151' Processing helix chain 'H' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE H 199 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LYS H 202 " --> pdb=" O ALA H 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE H 218 " --> pdb=" O GLN H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 246 removed outlier: 4.193A pdb=" N GLU H 244 " --> pdb=" O ARG H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 296 removed outlier: 5.685A pdb=" N ARG H 284 " --> pdb=" O MET H 280 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL H 288 " --> pdb=" O ARG H 284 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER H 289 " --> pdb=" O LYS H 285 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU H 290 " --> pdb=" O PHE H 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE H 294 " --> pdb=" O GLU H 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE H 295 " --> pdb=" O LEU H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL H 302 " --> pdb=" O PRO H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 326 Processing helix chain 'H' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE H 331 " --> pdb=" O LEU H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 348 Processing helix chain 'H' and resid 357 through 362 Processing helix chain 'H' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU H 377 " --> pdb=" O LYS H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP H 390 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 60 through 77 Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 112 through 128 Processing helix chain 'I' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE I 199 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS I 202 " --> pdb=" O ALA I 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER I 203 " --> pdb=" O PHE I 199 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE I 218 " --> pdb=" O GLN I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 247 Processing helix chain 'I' and resid 248 through 252 Processing helix chain 'I' and resid 279 through 296 removed outlier: 3.743A pdb=" N ARG I 284 " --> pdb=" O MET I 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL I 288 " --> pdb=" O ARG I 284 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER I 289 " --> pdb=" O LYS I 285 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU I 290 " --> pdb=" O PHE I 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE I 295 " --> pdb=" O LEU I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 326 Processing helix chain 'I' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE I 331 " --> pdb=" O LEU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 344 through 348 Processing helix chain 'I' and resid 357 through 362 Processing helix chain 'I' and resid 364 through 377 Processing helix chain 'I' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP I 390 " --> pdb=" O MET I 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 60 through 77 Processing helix chain 'J' and resid 97 through 105 Processing helix chain 'J' and resid 112 through 128 Processing helix chain 'J' and resid 149 through 151 No H-bonds generated for 'chain 'J' and resid 149 through 151' Processing helix chain 'J' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE J 199 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS J 202 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE J 218 " --> pdb=" O GLN J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 247 removed outlier: 3.551A pdb=" N GLN J 242 " --> pdb=" O GLN J 238 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL J 243 " --> pdb=" O GLN J 239 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU J 244 " --> pdb=" O ARG J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 296 removed outlier: 5.080A pdb=" N ARG J 284 " --> pdb=" O MET J 280 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL J 288 " --> pdb=" O ARG J 284 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER J 289 " --> pdb=" O LYS J 285 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU J 290 " --> pdb=" O PHE J 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE J 295 " --> pdb=" O LEU J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL J 302 " --> pdb=" O PRO J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 326 Processing helix chain 'J' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE J 331 " --> pdb=" O LEU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 348 Processing helix chain 'J' and resid 357 through 362 Processing helix chain 'J' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU J 377 " --> pdb=" O LYS J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP J 390 " --> pdb=" O MET J 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 60 through 77 Processing helix chain 'K' and resid 97 through 105 Processing helix chain 'K' and resid 112 through 128 Processing helix chain 'K' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE K 199 " --> pdb=" O SER K 195 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER K 203 " --> pdb=" O PHE K 199 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE K 218 " --> pdb=" O GLN K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 247 removed outlier: 3.965A pdb=" N GLU K 244 " --> pdb=" O ARG K 240 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU K 245 " --> pdb=" O SER K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 296 removed outlier: 3.987A pdb=" N SER K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU K 290 " --> pdb=" O PHE K 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE K 295 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 326 Processing helix chain 'K' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE K 331 " --> pdb=" O LEU K 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 344 through 348 Processing helix chain 'K' and resid 357 through 362 Processing helix chain 'K' and resid 364 through 377 Processing helix chain 'K' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP K 390 " --> pdb=" O MET K 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 60 through 77 Processing helix chain 'L' and resid 97 through 105 Processing helix chain 'L' and resid 112 through 128 Processing helix chain 'L' and resid 149 through 151 No H-bonds generated for 'chain 'L' and resid 149 through 151' Processing helix chain 'L' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS L 202 " --> pdb=" O ALA L 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER L 203 " --> pdb=" O PHE L 199 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 247 removed outlier: 3.899A pdb=" N VAL L 243 " --> pdb=" O GLN L 239 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU L 244 " --> pdb=" O ARG L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 296 removed outlier: 5.212A pdb=" N ARG L 284 " --> pdb=" O MET L 280 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL L 288 " --> pdb=" O ARG L 284 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER L 289 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU L 290 " --> pdb=" O PHE L 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE L 295 " --> pdb=" O LEU L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL L 302 " --> pdb=" O PRO L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 326 Processing helix chain 'L' and resid 327 through 342 removed outlier: 3.860A pdb=" N ILE L 331 " --> pdb=" O LEU L 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 344 through 348 Processing helix chain 'L' and resid 357 through 362 Processing helix chain 'L' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU L 377 " --> pdb=" O LYS L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP L 390 " --> pdb=" O MET L 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR A 131 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 133 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 145 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP A 135 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 158 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.528A pdb=" N SER A 269 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 136 removed outlier: 4.355A pdb=" N TYR B 131 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 158 Processing sheet with id=AA8, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AA9, first strand: chain 'B' and resid 259 through 260 removed outlier: 6.061A pdb=" N LEU B 259 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'C' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR C 131 " --> pdb=" O PRO C 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 133 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 145 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP C 135 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 153 through 158 Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 260 removed outlier: 6.874A pdb=" N LEU C 259 " --> pdb=" O LEU D 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 90 through 92 Processing sheet with id=AB6, first strand: chain 'D' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR D 131 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 153 through 158 Processing sheet with id=AB8, first strand: chain 'D' and resid 259 through 261 removed outlier: 5.959A pdb=" N LEU D 259 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AC1, first strand: chain 'E' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR E 131 " --> pdb=" O PRO E 147 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU E 133 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU E 145 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP E 135 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 153 through 158 Processing sheet with id=AC3, first strand: chain 'E' and resid 259 through 260 removed outlier: 6.079A pdb=" N LEU E 259 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 90 through 92 Processing sheet with id=AC5, first strand: chain 'F' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR F 131 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 153 through 158 Processing sheet with id=AC7, first strand: chain 'F' and resid 259 through 261 removed outlier: 5.554A pdb=" N LEU F 259 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC9, first strand: chain 'G' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR G 131 " --> pdb=" O PRO G 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU G 133 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU G 145 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP G 135 " --> pdb=" O ILE G 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 153 through 158 Processing sheet with id=AD2, first strand: chain 'G' and resid 259 through 260 removed outlier: 6.157A pdb=" N LEU G 259 " --> pdb=" O LEU H 228 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AD4, first strand: chain 'H' and resid 131 through 136 removed outlier: 4.355A pdb=" N TYR H 131 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 153 through 158 Processing sheet with id=AD6, first strand: chain 'H' and resid 259 through 260 removed outlier: 6.036A pdb=" N LEU H 259 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 90 through 92 Processing sheet with id=AD8, first strand: chain 'I' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR I 131 " --> pdb=" O PRO I 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU I 133 " --> pdb=" O LEU I 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU I 145 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP I 135 " --> pdb=" O ILE I 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 153 through 158 Processing sheet with id=AE1, first strand: chain 'I' and resid 259 through 260 removed outlier: 6.459A pdb=" N LEU I 259 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 90 through 92 Processing sheet with id=AE3, first strand: chain 'J' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR J 131 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 153 through 158 Processing sheet with id=AE5, first strand: chain 'J' and resid 259 through 260 removed outlier: 6.125A pdb=" N LEU J 259 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 90 through 92 Processing sheet with id=AE7, first strand: chain 'K' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR K 131 " --> pdb=" O PRO K 147 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU K 133 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU K 145 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP K 135 " --> pdb=" O ILE K 143 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 153 through 158 Processing sheet with id=AE9, first strand: chain 'K' and resid 259 through 260 removed outlier: 6.424A pdb=" N LEU K 259 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 90 through 92 Processing sheet with id=AF2, first strand: chain 'L' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR L 131 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 153 through 158 1549 hydrogen bonds defined for protein. 4461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.74 Time building geometry restraints manager: 9.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9842 1.33 - 1.45: 5439 1.45 - 1.58: 17707 1.58 - 1.70: 0 1.70 - 1.82: 312 Bond restraints: 33300 Sorted by residual: bond pdb=" CZ ARG E 387 " pdb=" NH2 ARG E 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.81e+00 bond pdb=" CZ ARG K 387 " pdb=" NH2 ARG K 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.81e+00 bond pdb=" CZ ARG A 387 " pdb=" NH2 ARG A 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.72e+00 bond pdb=" CZ ARG G 387 " pdb=" NH2 ARG G 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.72e+00 bond pdb=" CZ ARG C 387 " pdb=" NH2 ARG C 387 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.70e+00 ... (remaining 33295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 36607 2.28 - 4.57: 7618 4.57 - 6.85: 701 6.85 - 9.13: 45 9.13 - 11.41: 5 Bond angle restraints: 44976 Sorted by residual: angle pdb=" CA TRP J 260 " pdb=" CB TRP J 260 " pdb=" CG TRP J 260 " ideal model delta sigma weight residual 113.60 125.01 -11.41 1.90e+00 2.77e-01 3.61e+01 angle pdb=" OE1 GLN A 214 " pdb=" CD GLN A 214 " pdb=" NE2 GLN A 214 " ideal model delta sigma weight residual 122.60 116.79 5.81 1.00e+00 1.00e+00 3.37e+01 angle pdb=" OE1 GLN C 214 " pdb=" CD GLN C 214 " pdb=" NE2 GLN C 214 " ideal model delta sigma weight residual 122.60 116.86 5.74 1.00e+00 1.00e+00 3.30e+01 angle pdb=" OE1 GLN K 214 " pdb=" CD GLN K 214 " pdb=" NE2 GLN K 214 " ideal model delta sigma weight residual 122.60 116.89 5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" C SER K 229 " pdb=" N THR K 230 " pdb=" CA THR K 230 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 ... (remaining 44971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 18446 18.02 - 36.03: 1265 36.03 - 54.05: 309 54.05 - 72.06: 110 72.06 - 90.07: 66 Dihedral angle restraints: 20196 sinusoidal: 8244 harmonic: 11952 Sorted by residual: dihedral pdb=" C LYS F 248 " pdb=" N LYS F 248 " pdb=" CA LYS F 248 " pdb=" CB LYS F 248 " ideal model delta harmonic sigma weight residual -122.60 -139.00 16.40 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C LYS L 248 " pdb=" N LYS L 248 " pdb=" CA LYS L 248 " pdb=" CB LYS L 248 " ideal model delta harmonic sigma weight residual -122.60 -137.88 15.28 0 2.50e+00 1.60e-01 3.74e+01 dihedral pdb=" C LYS B 248 " pdb=" N LYS B 248 " pdb=" CA LYS B 248 " pdb=" CB LYS B 248 " ideal model delta harmonic sigma weight residual -122.60 -137.86 15.26 0 2.50e+00 1.60e-01 3.73e+01 ... (remaining 20193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 3970 0.118 - 0.236: 844 0.236 - 0.353: 60 0.353 - 0.471: 11 0.471 - 0.589: 11 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA LYS F 248 " pdb=" N LYS F 248 " pdb=" C LYS F 248 " pdb=" CB LYS F 248 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CA LYS L 248 " pdb=" N LYS L 248 " pdb=" C LYS L 248 " pdb=" CB LYS L 248 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" CA LYS B 248 " pdb=" N LYS B 248 " pdb=" C LYS B 248 " pdb=" CB LYS B 248 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.39e+00 ... (remaining 4893 not shown) Planarity restraints: 5904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 172 " 0.179 2.00e-02 2.50e+03 9.19e-02 1.69e+02 pdb=" CG TYR I 172 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR I 172 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR I 172 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR I 172 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR I 172 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR I 172 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR I 172 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 172 " -0.179 2.00e-02 2.50e+03 9.19e-02 1.69e+02 pdb=" CG TYR C 172 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR C 172 " 0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR C 172 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR C 172 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR C 172 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR C 172 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR C 172 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 172 " 0.179 2.00e-02 2.50e+03 9.17e-02 1.68e+02 pdb=" CG TYR K 172 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR K 172 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR K 172 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR K 172 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR K 172 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR K 172 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR K 172 " 0.115 2.00e-02 2.50e+03 ... (remaining 5901 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 42 1.99 - 2.72: 575 2.72 - 3.44: 51039 3.44 - 4.17: 78344 4.17 - 4.90: 138801 Nonbonded interactions: 268801 Sorted by model distance: nonbonded pdb=" CE LYS H 307 " pdb=" CB SER I 308 " model vdw 1.258 3.840 nonbonded pdb=" CE LYS B 307 " pdb=" CB SER C 308 " model vdw 1.258 3.840 nonbonded pdb=" CE LYS D 307 " pdb=" CB SER E 308 " model vdw 1.259 3.840 nonbonded pdb=" CE LYS J 307 " pdb=" CB SER K 308 " model vdw 1.259 3.840 nonbonded pdb=" CB SER A 308 " pdb=" CE LYS L 307 " model vdw 1.259 3.840 ... (remaining 268796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 69.150 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.041 33300 Z= 0.710 Angle : 1.783 11.414 44976 Z= 1.169 Chirality : 0.095 0.589 4896 Planarity : 0.016 0.150 5904 Dihedral : 15.334 90.075 12492 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 2.57 % Allowed : 6.64 % Favored : 90.79 % Rotamer: Outliers : 2.01 % Allowed : 6.94 % Favored : 91.04 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.12), residues: 4128 helix: -1.37 (0.10), residues: 1744 sheet: 0.26 (0.24), residues: 424 loop : -2.27 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.118 0.021 TRP F 260 HIS 0.013 0.004 HIS J 300 PHE 0.069 0.017 PHE K 218 TYR 0.179 0.022 TYR I 172 ARG 0.011 0.001 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.16397 ( 1549) hydrogen bonds : angle 8.19612 ( 4461) covalent geometry : bond 0.01186 (33300) covalent geometry : angle 1.78272 (44976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1122 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.6114 (OUTLIER) cc_final: 0.5586 (m-30) REVERT: A 89 ASN cc_start: 0.6561 (m-40) cc_final: 0.5740 (m-40) REVERT: A 244 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5285 (mm-30) REVERT: B 195 SER cc_start: 0.7796 (t) cc_final: 0.7547 (p) REVERT: B 232 GLU cc_start: 0.3631 (OUTLIER) cc_final: 0.3307 (pm20) REVERT: C 382 THR cc_start: 0.8621 (p) cc_final: 0.8178 (p) REVERT: D 88 ASP cc_start: 0.5990 (t0) cc_final: 0.5634 (t0) REVERT: D 220 ASN cc_start: 0.7524 (m-40) cc_final: 0.6933 (m110) REVERT: D 364 ASP cc_start: 0.4987 (OUTLIER) cc_final: 0.4442 (p0) REVERT: E 248 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.4968 (ttpp) REVERT: E 320 LEU cc_start: 0.8479 (mt) cc_final: 0.8207 (mt) REVERT: F 118 GLU cc_start: 0.7185 (tt0) cc_final: 0.6903 (tt0) REVERT: G 106 SER cc_start: 0.7910 (t) cc_final: 0.7223 (p) REVERT: H 280 MET cc_start: 0.7069 (tpp) cc_final: 0.6756 (tpp) REVERT: I 279 GLU cc_start: 0.5144 (OUTLIER) cc_final: 0.4716 (tt0) REVERT: J 223 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7975 (mtpp) REVERT: K 333 ARG cc_start: 0.5947 (mtt-85) cc_final: 0.5693 (mtm-85) REVERT: L 341 TRP cc_start: 0.8169 (m100) cc_final: 0.7732 (m100) outliers start: 71 outliers final: 20 residues processed: 1178 average time/residue: 0.5449 time to fit residues: 1000.2680 Evaluate side-chains 648 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 622 time to evaluate : 5.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 245 GLU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 228 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 208 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 86 GLN B 318 GLN C 86 GLN C 182 HIS C 226 GLN C 246 ASN D 86 GLN D 318 GLN D 352 HIS E 59 GLN E 86 GLN E 89 ASN E 324 GLN F 86 GLN F 87 ASN F 318 GLN G 86 GLN G 214 GLN G 242 GLN H 86 GLN H 149 GLN I 86 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN I 220 ASN I 318 GLN I 319 ASN J 86 GLN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 GLN J 324 GLN K 86 GLN K 220 ASN L 86 GLN L 89 ASN L 287 GLN L 318 GLN ** L 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.168293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140162 restraints weight = 46365.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143589 restraints weight = 27233.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145772 restraints weight = 19505.006| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33300 Z= 0.187 Angle : 0.783 9.589 44976 Z= 0.416 Chirality : 0.045 0.157 4896 Planarity : 0.005 0.042 5904 Dihedral : 7.481 108.552 4565 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.79 % Favored : 93.36 % Rotamer: Outliers : 3.74 % Allowed : 14.06 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 4128 helix: 0.45 (0.12), residues: 1756 sheet: -0.88 (0.19), residues: 688 loop : -1.57 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 311 HIS 0.006 0.001 HIS C 352 PHE 0.032 0.003 PHE H 186 TYR 0.020 0.002 TYR H 105 ARG 0.008 0.001 ARG J 362 Details of bonding type rmsd hydrogen bonds : bond 0.05301 ( 1549) hydrogen bonds : angle 5.62696 ( 4461) covalent geometry : bond 0.00418 (33300) covalent geometry : angle 0.78325 (44976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 701 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7963 (m-40) cc_final: 0.7658 (m-40) REVERT: A 242 GLN cc_start: 0.8167 (mm110) cc_final: 0.7631 (pp30) REVERT: C 85 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6579 (p0) REVERT: C 112 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8465 (p) REVERT: C 168 ARG cc_start: 0.7449 (ttp-170) cc_final: 0.6798 (ptt-90) REVERT: C 215 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7801 (ttp80) REVERT: C 347 ASP cc_start: 0.6060 (m-30) cc_final: 0.5711 (m-30) REVERT: D 88 ASP cc_start: 0.8145 (t0) cc_final: 0.7929 (t0) REVERT: D 212 ASP cc_start: 0.7229 (m-30) cc_final: 0.6996 (m-30) REVERT: D 215 ARG cc_start: 0.7824 (tmm-80) cc_final: 0.7577 (tmm-80) REVERT: D 216 ASP cc_start: 0.7458 (m-30) cc_final: 0.6620 (m-30) REVERT: D 220 ASN cc_start: 0.7803 (m-40) cc_final: 0.7526 (m-40) REVERT: D 346 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6018 (ptmt) REVERT: D 347 ASP cc_start: 0.7333 (m-30) cc_final: 0.7113 (m-30) REVERT: E 58 LEU cc_start: 0.8969 (tp) cc_final: 0.8736 (tt) REVERT: E 166 TYR cc_start: 0.7791 (t80) cc_final: 0.7431 (t80) REVERT: E 248 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.5638 (ttpp) REVERT: E 279 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.4365 (tm-30) REVERT: E 280 MET cc_start: 0.7381 (tpp) cc_final: 0.7082 (tpp) REVERT: F 111 MET cc_start: 0.6906 (mtt) cc_final: 0.6692 (mtt) REVERT: F 316 GLU cc_start: 0.8031 (tt0) cc_final: 0.7777 (tt0) REVERT: G 72 THR cc_start: 0.8554 (m) cc_final: 0.8054 (p) REVERT: G 76 CYS cc_start: 0.8302 (m) cc_final: 0.7702 (m) REVERT: G 214 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8090 (tm130) REVERT: G 392 MET cc_start: 0.6710 (mmm) cc_final: 0.6278 (mmm) REVERT: H 392 MET cc_start: 0.7465 (mmt) cc_final: 0.7085 (mmt) REVERT: I 143 ILE cc_start: 0.7611 (pt) cc_final: 0.7357 (tp) REVERT: I 168 ARG cc_start: 0.6786 (tpt170) cc_final: 0.6473 (tmt170) REVERT: I 215 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7343 (ttt90) REVERT: I 245 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7584 (tm-30) REVERT: I 261 ILE cc_start: 0.5890 (OUTLIER) cc_final: 0.5451 (pt) REVERT: I 318 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6725 (mt0) REVERT: J 350 ARG cc_start: 0.6705 (mtm110) cc_final: 0.6157 (ttp80) REVERT: K 184 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6560 (ttpt) REVERT: K 311 TRP cc_start: 0.3505 (OUTLIER) cc_final: 0.3037 (p90) REVERT: K 318 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7857 (tm-30) REVERT: L 318 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7150 (mm-40) outliers start: 132 outliers final: 67 residues processed: 799 average time/residue: 0.4447 time to fit residues: 566.8964 Evaluate side-chains 629 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 551 time to evaluate : 4.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 129 ASN Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 125 CYS Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 382 THR Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 184 LYS Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 110 TYR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 388 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 80 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 373 optimal weight: 0.9990 chunk 248 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 123 GLN B 214 GLN B 352 HIS C 89 ASN C 276 GLN D 239 GLN D 276 GLN E 182 HIS F 87 ASN F 214 GLN ** F 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 ASN G 242 GLN H 152 ASN H 182 HIS H 226 GLN H 242 GLN H 339 GLN I 129 ASN I 182 HIS I 214 GLN I 319 ASN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 324 GLN K 89 ASN L 89 ASN L 182 HIS L 287 GLN L 352 HIS ** L 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131294 restraints weight = 46865.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134643 restraints weight = 27470.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136754 restraints weight = 19726.775| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33300 Z= 0.164 Angle : 0.685 10.735 44976 Z= 0.362 Chirality : 0.044 0.158 4896 Planarity : 0.005 0.043 5904 Dihedral : 6.298 106.654 4537 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.08 % Favored : 93.19 % Rotamer: Outliers : 4.54 % Allowed : 15.65 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4128 helix: 0.80 (0.12), residues: 1744 sheet: -0.50 (0.21), residues: 588 loop : -1.42 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 311 HIS 0.007 0.002 HIS L 352 PHE 0.025 0.002 PHE E 186 TYR 0.018 0.002 TYR I 110 ARG 0.006 0.001 ARG J 362 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 1549) hydrogen bonds : angle 5.21406 ( 4461) covalent geometry : bond 0.00365 (33300) covalent geometry : angle 0.68457 (44976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 619 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8088 (mm110) cc_final: 0.7850 (pp30) REVERT: B 356 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7578 (t0) REVERT: C 168 ARG cc_start: 0.7377 (ttp-170) cc_final: 0.7081 (ptt-90) REVERT: C 368 ARG cc_start: 0.7520 (ptm160) cc_final: 0.7114 (ttp-170) REVERT: C 392 MET cc_start: 0.8062 (mmp) cc_final: 0.7450 (mmt) REVERT: D 88 ASP cc_start: 0.8167 (t0) cc_final: 0.7887 (t0) REVERT: D 212 ASP cc_start: 0.7271 (m-30) cc_final: 0.6919 (m-30) REVERT: D 213 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8471 (tm-30) REVERT: D 216 ASP cc_start: 0.7156 (m-30) cc_final: 0.6320 (m-30) REVERT: D 220 ASN cc_start: 0.8194 (m-40) cc_final: 0.7690 (m110) REVERT: D 354 GLU cc_start: 0.5867 (mt-10) cc_final: 0.5501 (mt-10) REVERT: E 248 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.5689 (ttpp) REVERT: E 301 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9098 (mt) REVERT: E 392 MET cc_start: 0.7681 (mmt) cc_final: 0.7259 (mpp) REVERT: F 111 MET cc_start: 0.7823 (mtt) cc_final: 0.7613 (mtt) REVERT: F 146 LEU cc_start: 0.8118 (tp) cc_final: 0.7883 (tp) REVERT: G 72 THR cc_start: 0.8913 (m) cc_final: 0.8226 (p) REVERT: G 73 LEU cc_start: 0.8805 (mm) cc_final: 0.8604 (mt) REVERT: G 76 CYS cc_start: 0.8453 (m) cc_final: 0.7925 (m) REVERT: G 178 LYS cc_start: 0.8058 (tptt) cc_final: 0.7829 (tppt) REVERT: G 356 ASN cc_start: 0.8280 (p0) cc_final: 0.8030 (p0) REVERT: G 392 MET cc_start: 0.7594 (mmm) cc_final: 0.7168 (mmm) REVERT: H 72 THR cc_start: 0.8780 (m) cc_final: 0.8500 (p) REVERT: H 76 CYS cc_start: 0.7984 (m) cc_final: 0.7608 (m) REVERT: H 171 GLU cc_start: 0.5802 (mp0) cc_final: 0.5321 (pp20) REVERT: H 392 MET cc_start: 0.7582 (mmt) cc_final: 0.6996 (mmt) REVERT: I 82 PHE cc_start: 0.7987 (m-80) cc_final: 0.7660 (m-10) REVERT: I 136 ARG cc_start: 0.7508 (ptp-170) cc_final: 0.7121 (ptp-110) REVERT: I 168 ARG cc_start: 0.6692 (tpt170) cc_final: 0.6220 (ttp-110) REVERT: I 215 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7254 (ttt90) REVERT: I 279 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.5687 (tm-30) REVERT: J 76 CYS cc_start: 0.7634 (m) cc_final: 0.6863 (p) REVERT: J 111 MET cc_start: 0.8353 (mtt) cc_final: 0.8085 (mtt) REVERT: J 350 ARG cc_start: 0.6949 (mtm110) cc_final: 0.6376 (ttp80) REVERT: K 91 LYS cc_start: 0.7807 (tppt) cc_final: 0.7580 (tptm) REVERT: K 311 TRP cc_start: 0.3771 (OUTLIER) cc_final: 0.3087 (p90) REVERT: K 318 GLN cc_start: 0.8485 (tm-30) cc_final: 0.7905 (tm-30) REVERT: K 375 MET cc_start: 0.7988 (mmt) cc_final: 0.7749 (mmt) REVERT: L 352 HIS cc_start: 0.6098 (t70) cc_final: 0.4823 (t-170) outliers start: 160 outliers final: 90 residues processed: 743 average time/residue: 0.4609 time to fit residues: 553.1690 Evaluate side-chains 598 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 502 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 302 VAL Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 135 ASP Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 110 TYR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 327 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 163 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 227 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 124 optimal weight: 0.0060 chunk 382 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 overall best weight: 2.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 226 GLN D 239 GLN E 214 GLN E 324 GLN F 87 ASN G 177 GLN G 242 GLN H 391 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 GLN I 220 ASN I 226 GLN I 318 GLN J 129 ASN J 246 ASN J 287 GLN J 391 ASN K 89 ASN L 276 GLN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 391 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.158260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130287 restraints weight = 46597.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133634 restraints weight = 27066.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135739 restraints weight = 19257.774| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33300 Z= 0.156 Angle : 0.645 8.221 44976 Z= 0.337 Chirality : 0.043 0.191 4896 Planarity : 0.004 0.045 5904 Dihedral : 6.037 117.373 4531 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.73 % Allowed : 5.55 % Favored : 93.73 % Rotamer: Outliers : 4.45 % Allowed : 16.55 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4128 helix: 0.86 (0.13), residues: 1741 sheet: -0.63 (0.20), residues: 681 loop : -1.26 (0.16), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 311 HIS 0.007 0.001 HIS H 300 PHE 0.022 0.002 PHE A 186 TYR 0.014 0.002 TYR J 164 ARG 0.007 0.001 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 1549) hydrogen bonds : angle 5.11390 ( 4461) covalent geometry : bond 0.00353 (33300) covalent geometry : angle 0.64512 (44976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 568 time to evaluate : 3.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7548 (m-40) cc_final: 0.7088 (m-40) REVERT: A 242 GLN cc_start: 0.8088 (mm110) cc_final: 0.7845 (pp30) REVERT: A 388 ARG cc_start: 0.8854 (mmm-85) cc_final: 0.8407 (mmm160) REVERT: B 280 MET cc_start: 0.8393 (tpt) cc_final: 0.8156 (tpt) REVERT: C 110 TYR cc_start: 0.8378 (m-80) cc_final: 0.8154 (m-80) REVERT: C 368 ARG cc_start: 0.7546 (ptm160) cc_final: 0.7238 (ttp-170) REVERT: C 392 MET cc_start: 0.8509 (mmp) cc_final: 0.8032 (mmt) REVERT: D 120 MET cc_start: 0.8397 (tpp) cc_final: 0.8033 (mmm) REVERT: D 212 ASP cc_start: 0.7320 (m-30) cc_final: 0.6826 (m-30) REVERT: D 215 ARG cc_start: 0.7777 (tmm-80) cc_final: 0.7249 (tmm-80) REVERT: D 216 ASP cc_start: 0.7046 (m-30) cc_final: 0.5985 (m-30) REVERT: D 220 ASN cc_start: 0.8272 (m-40) cc_final: 0.7836 (m110) REVERT: D 305 VAL cc_start: 0.4230 (OUTLIER) cc_final: 0.4006 (p) REVERT: E 58 LEU cc_start: 0.9270 (tp) cc_final: 0.8802 (tt) REVERT: E 248 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.5453 (ttpp) REVERT: F 153 MET cc_start: 0.6938 (mmm) cc_final: 0.6728 (tpp) REVERT: F 279 GLU cc_start: 0.5392 (mm-30) cc_final: 0.5188 (mm-30) REVERT: F 343 ILE cc_start: 0.8484 (mt) cc_final: 0.8208 (mt) REVERT: G 72 THR cc_start: 0.9022 (m) cc_final: 0.8170 (p) REVERT: G 73 LEU cc_start: 0.8888 (mm) cc_final: 0.8524 (mt) REVERT: G 76 CYS cc_start: 0.8298 (m) cc_final: 0.7629 (m) REVERT: G 178 LYS cc_start: 0.7961 (tptt) cc_final: 0.7712 (tppt) REVERT: G 279 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.5478 (tp30) REVERT: G 356 ASN cc_start: 0.8235 (p0) cc_final: 0.7758 (p0) REVERT: G 392 MET cc_start: 0.7815 (mmm) cc_final: 0.7497 (mmm) REVERT: H 58 LEU cc_start: 0.9108 (tp) cc_final: 0.8892 (tp) REVERT: H 72 THR cc_start: 0.8813 (m) cc_final: 0.8499 (p) REVERT: H 136 ARG cc_start: 0.5039 (ptp-110) cc_final: 0.4428 (ptm160) REVERT: H 171 GLU cc_start: 0.5948 (mp0) cc_final: 0.5561 (pp20) REVERT: H 392 MET cc_start: 0.7668 (mmt) cc_final: 0.6987 (mmt) REVERT: H 393 PRO cc_start: 0.8171 (Cg_exo) cc_final: 0.7481 (Cg_endo) REVERT: I 82 PHE cc_start: 0.7988 (m-80) cc_final: 0.7775 (m-10) REVERT: I 122 MET cc_start: 0.8793 (tpt) cc_final: 0.8524 (tpt) REVERT: I 136 ARG cc_start: 0.7557 (ptp-170) cc_final: 0.7184 (mtm110) REVERT: I 168 ARG cc_start: 0.6732 (tpt170) cc_final: 0.6296 (ttp-110) REVERT: I 215 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7264 (ttt90) REVERT: I 279 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.5449 (tm-30) REVERT: I 375 MET cc_start: 0.8708 (mmt) cc_final: 0.8484 (mmt) REVERT: J 76 CYS cc_start: 0.7716 (m) cc_final: 0.6996 (p) REVERT: J 168 ARG cc_start: 0.7081 (ptp-110) cc_final: 0.6804 (ttp-170) REVERT: K 311 TRP cc_start: 0.3863 (OUTLIER) cc_final: 0.3084 (p90) REVERT: K 318 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7951 (tm-30) REVERT: K 375 MET cc_start: 0.7776 (mmt) cc_final: 0.7441 (mmt) outliers start: 157 outliers final: 102 residues processed: 686 average time/residue: 0.4188 time to fit residues: 464.9342 Evaluate side-chains 614 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 506 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 125 CYS Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 129 ASN Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain L residue 367 SER Chi-restraints excluded: chain L residue 389 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 396 optimal weight: 0.0020 chunk 74 optimal weight: 9.9990 chunk 183 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 347 optimal weight: 0.9990 chunk 76 optimal weight: 30.0000 chunk 137 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 overall best weight: 1.0030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN C 318 GLN D 239 GLN E 214 GLN F 87 ASN F 242 GLN F 300 HIS G 242 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN J 129 ASN J 213 GLN J 352 HIS J 391 ASN K 287 GLN L 318 GLN L 352 HIS ** L 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133071 restraints weight = 46083.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.136580 restraints weight = 26140.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138814 restraints weight = 18303.709| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33300 Z= 0.115 Angle : 0.587 8.351 44976 Z= 0.306 Chirality : 0.041 0.249 4896 Planarity : 0.004 0.065 5904 Dihedral : 5.750 117.821 4531 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.89 % Favored : 93.51 % Rotamer: Outliers : 3.63 % Allowed : 18.88 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 4128 helix: 1.01 (0.13), residues: 1761 sheet: -0.34 (0.20), residues: 661 loop : -1.28 (0.16), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 311 HIS 0.010 0.001 HIS L 352 PHE 0.031 0.001 PHE H 186 TYR 0.019 0.001 TYR F 105 ARG 0.006 0.000 ARG D 388 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 1549) hydrogen bonds : angle 4.94980 ( 4461) covalent geometry : bond 0.00241 (33300) covalent geometry : angle 0.58727 (44976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 560 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7536 (m-40) cc_final: 0.6964 (t0) REVERT: A 167 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 188 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.7059 (t80) REVERT: A 242 GLN cc_start: 0.8093 (mm110) cc_final: 0.7821 (pp30) REVERT: A 388 ARG cc_start: 0.8842 (mmm-85) cc_final: 0.8415 (mmm160) REVERT: C 368 ARG cc_start: 0.7541 (ptm160) cc_final: 0.7301 (ttp-170) REVERT: D 120 MET cc_start: 0.8323 (tpp) cc_final: 0.7918 (mmm) REVERT: D 122 MET cc_start: 0.8268 (tpp) cc_final: 0.7809 (tpp) REVERT: D 153 MET cc_start: 0.8604 (tpp) cc_final: 0.8308 (tpt) REVERT: D 212 ASP cc_start: 0.7363 (m-30) cc_final: 0.6989 (m-30) REVERT: D 213 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8852 (tm-30) REVERT: D 216 ASP cc_start: 0.7081 (m-30) cc_final: 0.6358 (m-30) REVERT: D 220 ASN cc_start: 0.8260 (m-40) cc_final: 0.7759 (m110) REVERT: D 305 VAL cc_start: 0.4322 (OUTLIER) cc_final: 0.4109 (p) REVERT: D 375 MET cc_start: 0.8066 (mmm) cc_final: 0.7752 (mtt) REVERT: E 58 LEU cc_start: 0.9209 (tp) cc_final: 0.8821 (tt) REVERT: E 248 LYS cc_start: 0.6603 (OUTLIER) cc_final: 0.5549 (ttpp) REVERT: E 279 GLU cc_start: 0.5482 (OUTLIER) cc_final: 0.4627 (tm-30) REVERT: F 188 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6258 (t80) REVERT: G 72 THR cc_start: 0.9007 (m) cc_final: 0.8165 (p) REVERT: G 73 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8478 (mt) REVERT: G 76 CYS cc_start: 0.8277 (m) cc_final: 0.7753 (m) REVERT: G 80 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: G 153 MET cc_start: 0.8010 (tpp) cc_final: 0.7284 (tpp) REVERT: G 279 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5616 (tp30) REVERT: G 338 ILE cc_start: 0.8963 (mm) cc_final: 0.8685 (mt) REVERT: G 356 ASN cc_start: 0.8224 (p0) cc_final: 0.7789 (p0) REVERT: G 392 MET cc_start: 0.7815 (mmm) cc_final: 0.7319 (mmm) REVERT: H 72 THR cc_start: 0.8827 (m) cc_final: 0.8377 (p) REVERT: H 76 CYS cc_start: 0.7692 (m) cc_final: 0.7158 (m) REVERT: H 171 GLU cc_start: 0.5801 (mp0) cc_final: 0.5589 (pp20) REVERT: H 392 MET cc_start: 0.7628 (mmt) cc_final: 0.7095 (mmt) REVERT: H 393 PRO cc_start: 0.8237 (Cg_exo) cc_final: 0.7741 (Cg_endo) REVERT: I 82 PHE cc_start: 0.7861 (m-80) cc_final: 0.7649 (m-10) REVERT: I 122 MET cc_start: 0.8824 (tpt) cc_final: 0.8550 (tpt) REVERT: I 136 ARG cc_start: 0.7652 (ptp-170) cc_final: 0.7235 (mtm110) REVERT: I 168 ARG cc_start: 0.6721 (tpt170) cc_final: 0.6318 (ttp-110) REVERT: I 215 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7194 (ttt90) REVERT: I 279 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5178 (tm-30) REVERT: J 76 CYS cc_start: 0.7685 (m) cc_final: 0.6976 (p) REVERT: J 161 LYS cc_start: 0.8279 (ptpp) cc_final: 0.7543 (ptmt) REVERT: J 168 ARG cc_start: 0.7143 (ptp-110) cc_final: 0.6867 (ttp-170) REVERT: J 350 ARG cc_start: 0.7247 (mtm110) cc_final: 0.6760 (ttp80) REVERT: K 122 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7939 (tpt) REVERT: K 311 TRP cc_start: 0.3907 (OUTLIER) cc_final: 0.2845 (p90) REVERT: K 318 GLN cc_start: 0.8663 (tm-30) cc_final: 0.7944 (tm-30) REVERT: L 352 HIS cc_start: 0.5895 (t70) cc_final: 0.5295 (t-170) outliers start: 128 outliers final: 81 residues processed: 649 average time/residue: 0.4342 time to fit residues: 456.3462 Evaluate side-chains 606 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 513 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 110 TYR Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 313 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 131 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 375 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 389 optimal weight: 5.9990 chunk 302 optimal weight: 20.0000 chunk 73 optimal weight: 0.3980 chunk 169 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 318 GLN B 182 HIS D 318 GLN E 214 GLN E 220 ASN E 324 GLN F 87 ASN F 182 HIS G 182 HIS G 242 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 ASN J 213 GLN K 384 ASN L 318 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.153491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126054 restraints weight = 46263.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129376 restraints weight = 26123.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131454 restraints weight = 18293.178| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33300 Z= 0.199 Angle : 0.676 8.391 44976 Z= 0.353 Chirality : 0.045 0.252 4896 Planarity : 0.005 0.070 5904 Dihedral : 6.038 120.700 4529 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.54 % Favored : 92.85 % Rotamer: Outliers : 4.71 % Allowed : 18.34 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 4128 helix: 0.67 (0.12), residues: 1810 sheet: -0.16 (0.22), residues: 522 loop : -1.46 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 311 HIS 0.008 0.001 HIS H 300 PHE 0.022 0.002 PHE B 186 TYR 0.018 0.002 TYR E 330 ARG 0.006 0.001 ARG D 388 Details of bonding type rmsd hydrogen bonds : bond 0.05282 ( 1549) hydrogen bonds : angle 5.18696 ( 4461) covalent geometry : bond 0.00468 (33300) covalent geometry : angle 0.67601 (44976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 548 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7534 (m-40) cc_final: 0.6994 (t0) REVERT: A 122 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6980 (ttp) REVERT: A 188 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7101 (t80) REVERT: A 242 GLN cc_start: 0.8010 (mm110) cc_final: 0.7810 (pp30) REVERT: A 386 MET cc_start: 0.8323 (mmp) cc_final: 0.8035 (mmp) REVERT: A 388 ARG cc_start: 0.8867 (mmm-85) cc_final: 0.8341 (mmm160) REVERT: C 168 ARG cc_start: 0.6468 (ptt-90) cc_final: 0.5984 (ptt-90) REVERT: C 368 ARG cc_start: 0.7797 (ptm160) cc_final: 0.7452 (ttp-170) REVERT: D 120 MET cc_start: 0.8286 (tpp) cc_final: 0.8019 (mmm) REVERT: D 122 MET cc_start: 0.8373 (tpp) cc_final: 0.7890 (tpp) REVERT: D 212 ASP cc_start: 0.7412 (m-30) cc_final: 0.6964 (m-30) REVERT: D 216 ASP cc_start: 0.7207 (m-30) cc_final: 0.6490 (m-30) REVERT: D 220 ASN cc_start: 0.8303 (m-40) cc_final: 0.7850 (m-40) REVERT: D 232 GLU cc_start: 0.5625 (OUTLIER) cc_final: 0.3891 (mt-10) REVERT: D 277 ASP cc_start: 0.5126 (OUTLIER) cc_final: 0.4832 (t70) REVERT: E 58 LEU cc_start: 0.9322 (tp) cc_final: 0.8872 (tt) REVERT: E 188 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8204 (t80) REVERT: E 248 LYS cc_start: 0.6307 (OUTLIER) cc_final: 0.5647 (ttpp) REVERT: E 256 LYS cc_start: 0.6841 (mmtt) cc_final: 0.6491 (mtmm) REVERT: F 188 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6655 (t80) REVERT: G 72 THR cc_start: 0.9019 (m) cc_final: 0.8136 (p) REVERT: G 73 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8516 (mt) REVERT: G 76 CYS cc_start: 0.8148 (m) cc_final: 0.7547 (m) REVERT: G 279 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5902 (tp30) REVERT: G 356 ASN cc_start: 0.8455 (p0) cc_final: 0.8024 (p0) REVERT: H 72 THR cc_start: 0.8864 (m) cc_final: 0.8625 (p) REVERT: H 393 PRO cc_start: 0.8351 (Cg_exo) cc_final: 0.8088 (Cg_endo) REVERT: I 122 MET cc_start: 0.8793 (tpt) cc_final: 0.8546 (tpt) REVERT: I 136 ARG cc_start: 0.7871 (ptp-170) cc_final: 0.7452 (mtm110) REVERT: I 168 ARG cc_start: 0.6751 (tpt170) cc_final: 0.6331 (ttp-110) REVERT: I 215 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7308 (ttt90) REVERT: I 279 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5413 (tm-30) REVERT: J 122 MET cc_start: 0.7918 (tpp) cc_final: 0.7486 (ttt) REVERT: J 168 ARG cc_start: 0.7103 (ptp-110) cc_final: 0.6895 (ttp-170) REVERT: K 91 LYS cc_start: 0.8043 (tptt) cc_final: 0.7712 (tptm) REVERT: K 188 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7648 (t80) REVERT: K 311 TRP cc_start: 0.3853 (OUTLIER) cc_final: 0.3118 (p90) REVERT: K 318 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8005 (tm-30) REVERT: K 392 MET cc_start: 0.7806 (mmm) cc_final: 0.7425 (mmm) REVERT: L 167 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7597 (tm-30) outliers start: 166 outliers final: 112 residues processed: 670 average time/residue: 0.4438 time to fit residues: 477.8927 Evaluate side-chains 613 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 488 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 125 CYS Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain J residue 110 TYR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 129 ASN Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 388 ARG Chi-restraints excluded: chain L residue 389 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 83 optimal weight: 0.9990 chunk 402 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 387 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 160 optimal weight: 0.0870 chunk 349 optimal weight: 10.0000 chunk 310 optimal weight: 0.0050 chunk 378 optimal weight: 8.9990 overall best weight: 2.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 GLN E 324 GLN E 391 ASN G 242 GLN J 129 ASN J 213 GLN J 246 ASN L 318 GLN ** L 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.156240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128840 restraints weight = 46023.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132216 restraints weight = 25768.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.134377 restraints weight = 17965.374| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.7158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33300 Z= 0.136 Angle : 0.608 7.512 44976 Z= 0.318 Chirality : 0.042 0.233 4896 Planarity : 0.004 0.066 5904 Dihedral : 5.804 121.081 4529 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.01 % Favored : 93.39 % Rotamer: Outliers : 4.20 % Allowed : 19.27 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 4128 helix: 0.88 (0.13), residues: 1768 sheet: -0.06 (0.22), residues: 522 loop : -1.34 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 311 HIS 0.014 0.001 HIS L 352 PHE 0.027 0.002 PHE H 175 TYR 0.027 0.001 TYR E 105 ARG 0.007 0.000 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 1549) hydrogen bonds : angle 5.02254 ( 4461) covalent geometry : bond 0.00303 (33300) covalent geometry : angle 0.60843 (44976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 529 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7520 (m-40) cc_final: 0.7087 (t0) REVERT: A 122 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6813 (ttp) REVERT: A 167 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 188 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.7020 (t80) REVERT: A 386 MET cc_start: 0.8251 (mmp) cc_final: 0.7987 (mmp) REVERT: A 388 ARG cc_start: 0.8854 (mmm-85) cc_final: 0.8338 (mmm160) REVERT: B 115 GLU cc_start: 0.7935 (tp30) cc_final: 0.7572 (tp30) REVERT: C 168 ARG cc_start: 0.6237 (ptt-90) cc_final: 0.5966 (ptt-90) REVERT: C 368 ARG cc_start: 0.7749 (ptm160) cc_final: 0.7368 (ttp-170) REVERT: D 120 MET cc_start: 0.8382 (tpp) cc_final: 0.8111 (mmm) REVERT: D 188 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7652 (t80) REVERT: D 212 ASP cc_start: 0.7383 (m-30) cc_final: 0.6953 (m-30) REVERT: D 213 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8826 (tm-30) REVERT: D 216 ASP cc_start: 0.7111 (m-30) cc_final: 0.6409 (m-30) REVERT: D 220 ASN cc_start: 0.8295 (m-40) cc_final: 0.7865 (m-40) REVERT: D 232 GLU cc_start: 0.5665 (OUTLIER) cc_final: 0.4132 (mt-10) REVERT: D 354 GLU cc_start: 0.6281 (tp30) cc_final: 0.6049 (tp30) REVERT: D 368 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7723 (ttp-170) REVERT: E 58 LEU cc_start: 0.9298 (tp) cc_final: 0.8829 (tt) REVERT: E 160 LYS cc_start: 0.6102 (tptt) cc_final: 0.5451 (mttm) REVERT: E 188 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8206 (t80) REVERT: E 248 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5733 (ttpp) REVERT: E 256 LYS cc_start: 0.6806 (mmtt) cc_final: 0.6549 (mtmm) REVERT: E 279 GLU cc_start: 0.5634 (OUTLIER) cc_final: 0.4586 (tm-30) REVERT: F 167 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7622 (tt0) REVERT: F 188 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6749 (t80) REVERT: G 72 THR cc_start: 0.9023 (m) cc_final: 0.8090 (p) REVERT: G 73 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8533 (mt) REVERT: G 76 CYS cc_start: 0.8112 (m) cc_final: 0.7406 (m) REVERT: G 279 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5850 (tp30) REVERT: G 316 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: G 356 ASN cc_start: 0.8425 (p0) cc_final: 0.7911 (p0) REVERT: G 392 MET cc_start: 0.7421 (mmm) cc_final: 0.7125 (mmm) REVERT: H 178 LYS cc_start: 0.8381 (pttm) cc_final: 0.8092 (pttp) REVERT: H 326 THR cc_start: 0.9320 (m) cc_final: 0.8945 (p) REVERT: H 393 PRO cc_start: 0.8387 (Cg_exo) cc_final: 0.8136 (Cg_endo) REVERT: I 122 MET cc_start: 0.8745 (tpt) cc_final: 0.8501 (tpt) REVERT: I 136 ARG cc_start: 0.7825 (ptp-170) cc_final: 0.6837 (mtt-85) REVERT: I 168 ARG cc_start: 0.6685 (tpt170) cc_final: 0.6283 (ttp-110) REVERT: I 215 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7211 (ttt90) REVERT: I 279 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5016 (tm-30) REVERT: J 122 MET cc_start: 0.7828 (tpp) cc_final: 0.7330 (ttt) REVERT: J 129 ASN cc_start: 0.9316 (OUTLIER) cc_final: 0.9009 (m110) REVERT: K 91 LYS cc_start: 0.8005 (tptt) cc_final: 0.7534 (tptm) REVERT: K 188 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7752 (t80) REVERT: K 311 TRP cc_start: 0.3906 (OUTLIER) cc_final: 0.2770 (p90) REVERT: K 318 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8002 (tm-30) REVERT: K 392 MET cc_start: 0.7798 (mmm) cc_final: 0.7377 (mmm) REVERT: L 167 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 148 outliers final: 103 residues processed: 641 average time/residue: 0.4594 time to fit residues: 475.9963 Evaluate side-chains 614 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 495 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 263 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 129 ASN Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 260 TRP Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 188 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 389 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 232 optimal weight: 0.9990 chunk 259 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 396 optimal weight: 9.9990 chunk 190 optimal weight: 0.0060 chunk 227 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 GLN E 324 GLN E 384 ASN G 242 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN J 129 ASN J 391 ASN L 318 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.159898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132717 restraints weight = 45642.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136190 restraints weight = 25299.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138358 restraints weight = 17447.519| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.7336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33300 Z= 0.112 Angle : 0.586 8.486 44976 Z= 0.304 Chirality : 0.041 0.228 4896 Planarity : 0.004 0.057 5904 Dihedral : 5.517 123.276 4528 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.20 % Favored : 93.17 % Rotamer: Outliers : 3.43 % Allowed : 20.12 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4128 helix: 1.02 (0.13), residues: 1768 sheet: 0.26 (0.21), residues: 562 loop : -1.34 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 311 HIS 0.016 0.001 HIS L 352 PHE 0.030 0.001 PHE H 175 TYR 0.020 0.001 TYR E 105 ARG 0.006 0.000 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 1549) hydrogen bonds : angle 4.86840 ( 4461) covalent geometry : bond 0.00235 (33300) covalent geometry : angle 0.58610 (44976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 552 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7436 (m-40) cc_final: 0.7039 (t0) REVERT: A 188 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7072 (t80) REVERT: A 386 MET cc_start: 0.8132 (mmp) cc_final: 0.7904 (mmp) REVERT: A 388 ARG cc_start: 0.8806 (mmm-85) cc_final: 0.8392 (mmm160) REVERT: B 115 GLU cc_start: 0.7889 (tp30) cc_final: 0.7538 (tp30) REVERT: B 172 TYR cc_start: 0.7096 (m-80) cc_final: 0.6763 (m-80) REVERT: C 122 MET cc_start: 0.8233 (tpt) cc_final: 0.7983 (tpt) REVERT: C 368 ARG cc_start: 0.7671 (ptm160) cc_final: 0.7337 (ttp-170) REVERT: D 120 MET cc_start: 0.8334 (tpp) cc_final: 0.8038 (mmm) REVERT: D 122 MET cc_start: 0.8293 (tpp) cc_final: 0.7876 (tpp) REVERT: D 212 ASP cc_start: 0.7315 (m-30) cc_final: 0.6882 (m-30) REVERT: D 213 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8619 (tm-30) REVERT: D 216 ASP cc_start: 0.7075 (m-30) cc_final: 0.6300 (m-30) REVERT: D 220 ASN cc_start: 0.8254 (m-40) cc_final: 0.7800 (m-40) REVERT: D 232 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.4358 (mt-10) REVERT: E 58 LEU cc_start: 0.9241 (tp) cc_final: 0.8815 (tt) REVERT: E 160 LYS cc_start: 0.6073 (tptt) cc_final: 0.5439 (mttm) REVERT: E 248 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5841 (ttpp) REVERT: E 279 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.4668 (tm-30) REVERT: F 105 TYR cc_start: 0.8604 (t80) cc_final: 0.8349 (t80) REVERT: F 167 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7698 (tt0) REVERT: G 72 THR cc_start: 0.9026 (m) cc_final: 0.8069 (p) REVERT: G 73 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8601 (mt) REVERT: G 76 CYS cc_start: 0.8055 (m) cc_final: 0.7347 (m) REVERT: G 279 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5612 (tp30) REVERT: G 356 ASN cc_start: 0.8343 (p0) cc_final: 0.7866 (p0) REVERT: H 178 LYS cc_start: 0.8365 (pttm) cc_final: 0.8096 (pttp) REVERT: H 393 PRO cc_start: 0.8432 (Cg_exo) cc_final: 0.8215 (Cg_endo) REVERT: I 122 MET cc_start: 0.8688 (tpt) cc_final: 0.8454 (tpt) REVERT: I 279 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.4797 (tm-30) REVERT: J 122 MET cc_start: 0.7745 (tpp) cc_final: 0.7362 (ttt) REVERT: K 91 LYS cc_start: 0.7934 (tptt) cc_final: 0.7493 (tptm) REVERT: K 122 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8033 (tpt) REVERT: K 227 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7247 (mp) REVERT: K 311 TRP cc_start: 0.3635 (OUTLIER) cc_final: 0.2615 (p90) REVERT: K 318 GLN cc_start: 0.8611 (tm-30) cc_final: 0.7968 (tm-30) REVERT: K 392 MET cc_start: 0.7792 (mmm) cc_final: 0.7300 (mmt) REVERT: L 167 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7341 (tm-30) REVERT: L 188 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7662 (t80) outliers start: 121 outliers final: 85 residues processed: 637 average time/residue: 0.4198 time to fit residues: 431.4920 Evaluate side-chains 598 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 502 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 263 GLU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain J residue 110 TYR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 260 TRP Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 110 TYR Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 188 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 229 optimal weight: 0.8980 chunk 349 optimal weight: 10.0000 chunk 366 optimal weight: 4.9990 chunk 344 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 384 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 352 HIS E 214 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 GLN J 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.153882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126571 restraints weight = 45988.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129904 restraints weight = 25694.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132032 restraints weight = 17929.577| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.7479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33300 Z= 0.171 Angle : 0.644 8.473 44976 Z= 0.334 Chirality : 0.044 0.243 4896 Planarity : 0.005 0.065 5904 Dihedral : 5.687 126.222 4526 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.71 % Favored : 92.66 % Rotamer: Outliers : 3.66 % Allowed : 20.38 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 4128 helix: 0.81 (0.12), residues: 1810 sheet: -0.08 (0.21), residues: 592 loop : -1.39 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 311 HIS 0.016 0.002 HIS L 352 PHE 0.033 0.002 PHE H 175 TYR 0.022 0.002 TYR E 105 ARG 0.010 0.001 ARG E 215 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 1549) hydrogen bonds : angle 5.00877 ( 4461) covalent geometry : bond 0.00400 (33300) covalent geometry : angle 0.64388 (44976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 517 time to evaluate : 4.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7461 (m-40) cc_final: 0.7066 (t0) REVERT: A 122 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6938 (ttp) REVERT: A 167 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7771 (tm-30) REVERT: A 188 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7105 (t80) REVERT: A 388 ARG cc_start: 0.8883 (mmm-85) cc_final: 0.8408 (mmm160) REVERT: C 188 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8231 (t80) REVERT: C 240 ARG cc_start: 0.7565 (tpp80) cc_final: 0.6992 (ptp-170) REVERT: D 120 MET cc_start: 0.8244 (tpp) cc_final: 0.8027 (mmm) REVERT: D 122 MET cc_start: 0.8268 (tpp) cc_final: 0.7951 (tpp) REVERT: D 212 ASP cc_start: 0.7378 (m-30) cc_final: 0.6924 (m-30) REVERT: D 213 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8559 (tm-30) REVERT: D 216 ASP cc_start: 0.7187 (m-30) cc_final: 0.6535 (m-30) REVERT: D 220 ASN cc_start: 0.8358 (m-40) cc_final: 0.7888 (m-40) REVERT: D 232 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.4231 (mt-10) REVERT: E 160 LYS cc_start: 0.6181 (tptt) cc_final: 0.5580 (mttm) REVERT: E 248 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5973 (ttpp) REVERT: E 256 LYS cc_start: 0.6713 (mtmm) cc_final: 0.5762 (tttm) REVERT: E 279 GLU cc_start: 0.5425 (OUTLIER) cc_final: 0.4389 (tm-30) REVERT: F 167 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7777 (tt0) REVERT: G 72 THR cc_start: 0.9043 (m) cc_final: 0.8126 (p) REVERT: G 73 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8553 (mt) REVERT: G 76 CYS cc_start: 0.8089 (m) cc_final: 0.7410 (m) REVERT: G 279 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.5854 (tp30) REVERT: G 356 ASN cc_start: 0.8357 (p0) cc_final: 0.7937 (p0) REVERT: H 167 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7311 (mt0) REVERT: H 375 MET cc_start: 0.8950 (mmt) cc_final: 0.8690 (mmt) REVERT: H 393 PRO cc_start: 0.8641 (Cg_exo) cc_final: 0.8429 (Cg_endo) REVERT: I 242 GLN cc_start: 0.6934 (tp40) cc_final: 0.6294 (mt0) REVERT: I 279 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5412 (tm-30) REVERT: I 389 THR cc_start: 0.8873 (m) cc_final: 0.8619 (p) REVERT: J 122 MET cc_start: 0.7642 (tpp) cc_final: 0.7387 (ttt) REVERT: K 91 LYS cc_start: 0.8034 (tptt) cc_final: 0.7593 (tptm) REVERT: K 227 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7590 (mp) REVERT: K 311 TRP cc_start: 0.4000 (OUTLIER) cc_final: 0.2892 (p90) REVERT: K 318 GLN cc_start: 0.8717 (tm-30) cc_final: 0.7975 (tm-30) REVERT: K 392 MET cc_start: 0.7865 (mmm) cc_final: 0.7429 (mmt) REVERT: L 111 MET cc_start: 0.8100 (mtm) cc_final: 0.7758 (mtm) REVERT: L 167 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7470 (tm-30) outliers start: 129 outliers final: 97 residues processed: 611 average time/residue: 0.7575 time to fit residues: 765.1102 Evaluate side-chains 596 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 488 time to evaluate : 6.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 263 GLU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain J residue 110 TYR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 260 TRP Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 188 PHE Chi-restraints excluded: chain L residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 64 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 320 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 343 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 275 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 276 GLN A 339 GLN ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN E 214 GLN E 324 GLN F 242 GLN F 391 ASN G 182 HIS I 177 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 GLN J 391 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123063 restraints weight = 46377.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126328 restraints weight = 26141.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128397 restraints weight = 18331.013| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.7733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33300 Z= 0.230 Angle : 0.717 10.655 44976 Z= 0.371 Chirality : 0.046 0.250 4896 Planarity : 0.005 0.076 5904 Dihedral : 6.044 128.360 4526 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.81 % Favored : 92.49 % Rotamer: Outliers : 3.54 % Allowed : 20.80 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 4128 helix: 0.55 (0.12), residues: 1806 sheet: -0.27 (0.22), residues: 588 loop : -1.51 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 311 HIS 0.011 0.002 HIS L 352 PHE 0.036 0.002 PHE H 175 TYR 0.022 0.002 TYR E 105 ARG 0.008 0.001 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.05404 ( 1549) hydrogen bonds : angle 5.23495 ( 4461) covalent geometry : bond 0.00544 (33300) covalent geometry : angle 0.71681 (44976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 503 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7490 (m-40) cc_final: 0.7089 (t0) REVERT: A 111 MET cc_start: 0.8655 (mtt) cc_final: 0.8409 (mtm) REVERT: A 122 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7029 (ttp) REVERT: A 167 GLN cc_start: 0.8256 (tm130) cc_final: 0.7660 (tm-30) REVERT: A 188 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7158 (t80) REVERT: A 388 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8366 (mmm160) REVERT: C 233 LYS cc_start: 0.4705 (ttpp) cc_final: 0.4395 (ttmt) REVERT: C 240 ARG cc_start: 0.7502 (tpp80) cc_final: 0.6997 (ptp-170) REVERT: C 368 ARG cc_start: 0.7922 (ptm160) cc_final: 0.7502 (ttp-170) REVERT: D 88 ASP cc_start: 0.7912 (t0) cc_final: 0.7633 (p0) REVERT: D 212 ASP cc_start: 0.7373 (m-30) cc_final: 0.6958 (m-30) REVERT: D 216 ASP cc_start: 0.7219 (m-30) cc_final: 0.6658 (m-30) REVERT: D 220 ASN cc_start: 0.8402 (m-40) cc_final: 0.7998 (m-40) REVERT: D 232 GLU cc_start: 0.5638 (OUTLIER) cc_final: 0.4110 (mt-10) REVERT: E 58 LEU cc_start: 0.9343 (tp) cc_final: 0.8858 (tt) REVERT: E 166 TYR cc_start: 0.8266 (t80) cc_final: 0.7976 (t80) REVERT: E 279 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.4849 (tt0) REVERT: G 72 THR cc_start: 0.9074 (m) cc_final: 0.8322 (p) REVERT: G 73 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8498 (mt) REVERT: G 76 CYS cc_start: 0.8027 (m) cc_final: 0.7343 (m) REVERT: G 279 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5773 (tp30) REVERT: G 356 ASN cc_start: 0.8334 (p0) cc_final: 0.7960 (p0) REVERT: H 165 ARG cc_start: 0.7627 (tpt-90) cc_final: 0.7344 (tpp80) REVERT: H 167 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7412 (mt0) REVERT: I 122 MET cc_start: 0.8785 (tpt) cc_final: 0.8553 (tpt) REVERT: I 279 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5498 (tm-30) REVERT: J 111 MET cc_start: 0.8420 (mtt) cc_final: 0.7967 (mtt) REVERT: J 122 MET cc_start: 0.7720 (tpp) cc_final: 0.7331 (ttt) REVERT: J 157 LEU cc_start: 0.6317 (pt) cc_final: 0.6024 (tp) REVERT: K 91 LYS cc_start: 0.8198 (tptt) cc_final: 0.7737 (tptm) REVERT: K 136 ARG cc_start: 0.7560 (ptm160) cc_final: 0.6983 (ptp90) REVERT: K 311 TRP cc_start: 0.4158 (OUTLIER) cc_final: 0.3342 (p-90) REVERT: K 318 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8017 (tm-30) REVERT: K 392 MET cc_start: 0.7914 (mmm) cc_final: 0.7491 (mmt) REVERT: L 167 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7562 (tm-30) outliers start: 125 outliers final: 96 residues processed: 601 average time/residue: 0.4727 time to fit residues: 456.1717 Evaluate side-chains 585 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 481 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 263 GLU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 110 TYR Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 188 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 398 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 376 optimal weight: 1.9990 chunk 365 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 343 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 255 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 318 GLN D 352 HIS E 214 GLN E 324 GLN F 167 GLN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 GLN J 220 ASN J 391 ASN K 220 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126612 restraints weight = 45801.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129966 restraints weight = 25630.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132096 restraints weight = 17844.517| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.7834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33300 Z= 0.153 Angle : 0.644 8.981 44976 Z= 0.332 Chirality : 0.043 0.251 4896 Planarity : 0.004 0.070 5904 Dihedral : 5.709 127.035 4522 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.64 % Favored : 92.71 % Rotamer: Outliers : 3.09 % Allowed : 21.71 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.13), residues: 4128 helix: 0.76 (0.12), residues: 1770 sheet: -0.26 (0.22), residues: 588 loop : -1.47 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 311 HIS 0.020 0.001 HIS L 352 PHE 0.030 0.002 PHE H 175 TYR 0.021 0.002 TYR E 105 ARG 0.009 0.000 ARG G 168 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 1549) hydrogen bonds : angle 5.08914 ( 4461) covalent geometry : bond 0.00353 (33300) covalent geometry : angle 0.64400 (44976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12403.96 seconds wall clock time: 219 minutes 8.67 seconds (13148.67 seconds total)